Genomic structure of Bali cattle based on linkage disequilibrium and effective population size analyses using 50K single nucleotide polymorphisms data

Pita Sudrajad,Slamet Diah Volkandari,Richi Yuliavian Kusminanto,Muhammad Cahyadi

doi:10.14202/vetworld.2022.449-454

Abstract

Background and aim:Bali Cattle (Bos j. javanicus) is a local breed originating in Indonesia, accounting for 32.3% of the total cattle population. To date, no studies of the genetic structure and demographic status of Bali cattle have been conducted, even though the breeding of Bali cattle has a long and unique history that is likely to have impacted its genetic diversity. Therefore, a study that used molecular breeding technologies to characterize the demography of Bali cattle would be timely. This study aimed to examine genome diversity in Bali cattle and estimate the linkage disequilibrium (LD) and effective population size (Ne) values in the cattle population.Materials and Methods:In this study, we explored the population structure and genetic diversity of Bali cattle using genomic-level analyses. Our study primarily studied cattle that had been bred in livestock breeding centers since these breeds had subsequently spread throughout Indonesia. We focused on characterizing the genetic structure, determining the level of LD present, and estimating the Ne of the Bali cattle population. The genomic data used for this study were obtained from DNA samples of 48 Bali cattle collected at the Breeding Center of Bali Cattle as well as 54 genomic samples from Bali cattle collected elsewhere in Indonesia that had been used in recent publications. This genomic dataset included exclusively 50K single nucleotide polymorphisms (SNP) array (Illumina Bovine 50SNP bead chip, Illumina, USA) data.Results:We found that the LD values of Bali cattle from the breeding center and those raised elsewhere were 0.48±0.43 and 0.39±0.40, respectively. Subsequently, the Ne value of Bali cattle from the breeding center and farmers was 151 and 96, respectively.Conclusion:Our results suggest that the selection program of the breeding center is beneficial for maintaining the genetic diversity of Bali cattle.

Highlights

Bali cattle (Bos j. javanicus) have a unique history and genetic background, as they are the only native Indonesian cattle that were domesticated by the Banteng [1,2]
We focused on characterizing the genetic structure, determining the level of linkage disequilibrium (LD) present, and estimating the Ne of the Bali cattle population
The genomic data used for this study were obtained from DNA samples of 48 Bali cattle collected at the Breeding Center of Bali Cattle as well as 54 genomic samples from Bali cattle collected elsewhere in Indonesia that had been used in recent publications

Summary

Introduction

Bali cattle (Bos j. javanicus) have a unique history and genetic background, as they are the only native Indonesian cattle that were domesticated by the Banteng [1,2]. Bali cattle are the most suitable for several regions in Indonesia because they possess unique adaptations to the tropical environment, including a high growth rate even when given low-quality feed [2]. These characteristics make Bali cattle attractive for farming in Indonesia; at the time of the last census, Bali cattle were the predominant breed in Indonesia, representing 32.3% of all cattle in the country [3]. No studies of the genetic structure and demographic status of Bali cattle have been conducted, even though the breeding of Bali cattle has a long and unique history that is likely to have impacted its genetic diversity. This study aimed to examine genome diversity in Bali cattle and estimate the linkage disequilibrium (LD) and effective population size (Ne) values in the cattle population

Objectives

Methods

Results

Conclusion